151
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Correction of β-thalassemia by CRISPR/Cas9 editing of the α-globin locus in human hematopoietic stem cells. Blood Adv 2021; 5:1137-1153. [PMID: 33635334 DOI: 10.1182/bloodadvances.2020001996] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
β-thalassemias (β-thal) are a group of blood disorders caused by mutations in the β-globin gene (HBB) cluster. β-globin associates with α-globin to form adult hemoglobin (HbA, α2β2), the main oxygen-carrier in erythrocytes. When β-globin chains are absent or limiting, free α-globins precipitate and damage cell membranes, causing hemolysis and ineffective erythropoiesis. Clinical data show that severity of β-thal correlates with the number of inherited α-globin genes (HBA1 and HBA2), with α-globin gene deletions having a beneficial effect for patients. Here, we describe a novel strategy to treat β-thal based on genome editing of the α-globin locus in human hematopoietic stem/progenitor cells (HSPCs). Using CRISPR/Cas9, we combined 2 therapeutic approaches: (1) α-globin downregulation, by deleting the HBA2 gene to recreate an α-thalassemia trait, and (2) β-globin expression, by targeted integration of a β-globin transgene downstream the HBA2 promoter. First, we optimized the CRISPR/Cas9 strategy and corrected the pathological phenotype in a cellular model of β-thalassemia (human erythroid progenitor cell [HUDEP-2] β0). Then, we edited healthy donor HSPCs and demonstrated that they maintained long-term repopulation capacity and multipotency in xenotransplanted mice. To assess the clinical potential of this approach, we next edited β-thal HSPCs and achieved correction of α/β globin imbalance in HSPC-derived erythroblasts. As a safer option for clinical translation, we performed editing in HSPCs using Cas9 nickase showing precise editing with no InDels. Overall, we described an innovative CRISPR/Cas9 approach to improve α/β globin imbalance in thalassemic HSPCs, paving the way for novel therapeutic strategies for β-thal.
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152
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Jaschke N, Sipos W, Hofbauer LC, Rachner TD, Rauner M. Skeletal endocrinology: where evolutionary advantage meets disease. Bone Res 2021; 9:28. [PMID: 34050126 PMCID: PMC8163738 DOI: 10.1038/s41413-021-00149-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/16/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023] Open
Abstract
The regulation of whole-body homeostasis by the skeleton is mediated by its capacity to secrete endocrine signaling molecules. Although bone-derived hormones confer several adaptive benefits, their physiological functions also involve trade-offs, thus eventually contributing to disease. In this manuscript, we discuss the origins and functions of two of the best-studied skeletal mediators, fibroblast growth factor 23 and osteocalcin, in an evolutionary context. Moreover, we provide a theoretical framework seeking to explain the broad involvement of these two hormones in amniote physiology as well as their potential to fuel the development and progression of diseases. Vice versa, we outline which perturbations might be amenable to manipulation of these systems and discuss limitations and ongoing challenges in skeletal endocrine research. Finally, we summarize unresolved questions and potential future studies in this thriving field.
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Affiliation(s)
- Nikolai Jaschke
- Department of Medicine III & Center for Healthy Aging, Technische Universität Dresden, Dresden, Germany
| | - Wolfgang Sipos
- Clinical Department for Farm Animals, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Lorenz C Hofbauer
- Department of Medicine III & Center for Healthy Aging, Technische Universität Dresden, Dresden, Germany
| | - Tilman D Rachner
- Department of Medicine III & Center for Healthy Aging, Technische Universität Dresden, Dresden, Germany
| | - Martina Rauner
- Department of Medicine III & Center for Healthy Aging, Technische Universität Dresden, Dresden, Germany.
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153
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Escobar H, Krause A, Keiper S, Kieshauer J, Müthel S, de Paredes MG, Metzler E, Kühn R, Heyd F, Spuler S. Base editing repairs an SGCA mutation in human primary muscle stem cells. JCI Insight 2021; 6:145994. [PMID: 33848270 PMCID: PMC8262330 DOI: 10.1172/jci.insight.145994] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/07/2021] [Indexed: 11/28/2022] Open
Abstract
Skeletal muscle can regenerate from muscle stem cells and their myogenic precursor cell progeny, myoblasts. However, precise gene editing in human muscle stem cells for autologous cell replacement therapies of untreatable genetic muscle diseases has not yet been reported. Loss-of-function mutations in SGCA, encoding α-sarcoglycan, cause limb-girdle muscular dystrophy 2D/R3, an early-onset, severe, and rapidly progressive form of muscular dystrophy affecting both male and female patients. Patients suffer from muscle degeneration and atrophy affecting the limbs, respiratory muscles, and heart. We isolated human muscle stem cells from 2 donors, with the common SGCA c.157G>A mutation affecting the last coding nucleotide of exon 2. We found that c.157G>A is an exonic splicing mutation that induces skipping of 2 coregulated exons. Using adenine base editing, we corrected the mutation in the cells from both donors with > 90% efficiency, thereby rescuing the splicing defect and α-sarcoglycan expression. Base-edited patient cells regenerated muscle and contributed to the Pax7+ satellite cell compartment in vivo in mouse xenografts. Here, we provide the first evidence to our knowledge that autologous gene–repaired human muscle stem cells can be harnessed for cell replacement therapies of muscular dystrophies.
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Affiliation(s)
- Helena Escobar
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany.,Charité Universitätsmedizin Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anne Krause
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany.,Charité Universitätsmedizin Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Sandra Keiper
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Berlin, Germany
| | - Janine Kieshauer
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany.,Charité Universitätsmedizin Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Stefanie Müthel
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany.,Charité Universitätsmedizin Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Manuel García de Paredes
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany
| | - Eric Metzler
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany.,Charité Universitätsmedizin Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Berlin, Germany
| | - Simone Spuler
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany
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154
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Abstract
In this issue of Cell, Zuccaro and colleagues show that on-target Cas9-mediated double-strand breaks cause chromosome loss or mis-repair of the disease allele in > 90% of human embryos. End joining repair pathways dominate, causing small insertions or deletions, which raises serious questions about using double-strand breaks for "gene surgery".
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Affiliation(s)
- Eva R Hoffmann
- Danish National Research Foundation Center for Chromosome Stability, Department of Cellular and Molecular Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Ignasi Roig
- Unitat de Citologia i Histologia, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain; Grup d'Inestabilitat i Integritat del Genoma, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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155
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Zhang X, Li T, Ou J, Huang J, Liang P. Homology-based repair induced by CRISPR-Cas nucleases in mammalian embryo genome editing. Protein Cell 2021; 13:316-335. [PMID: 33945139 PMCID: PMC9008090 DOI: 10.1007/s13238-021-00838-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/16/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in genome editing, especially CRISPR-Cas nucleases, have revolutionized both laboratory research and clinical therapeutics. CRISPR-Cas nucleases, together with the DNA damage repair pathway in cells, enable both genetic diversification by classical non-homologous end joining (c-NHEJ) and precise genome modification by homology-based repair (HBR). Genome editing in zygotes is a convenient way to edit the germline, paving the way for animal disease model generation, as well as human embryo genome editing therapy for some life-threatening and incurable diseases. HBR efficiency is highly dependent on the DNA donor that is utilized as a repair template. Here, we review recent progress in improving CRISPR-Cas nuclease-induced HBR in mammalian embryos by designing a suitable DNA donor. Moreover, we want to provide a guide for producing animal disease models and correcting genetic mutations through CRISPR-Cas nuclease-induced HBR in mammalian embryos. Finally, we discuss recent developments in precise genome-modification technology based on the CRISPR-Cas system.
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Affiliation(s)
- Xiya Zhang
- Center for Reproductive Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, 510630, China
| | - Tao Li
- Center for Reproductive Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, 510630, China
| | - Jianping Ou
- Center for Reproductive Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, 510630, China.
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Puping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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156
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Froehlich JJ, Uyar B, Herzog M, Theil K, Glažar P, Akalin A, Rajewsky N. Parallel genetics of regulatory sequences using scalable genome editing in vivo. Cell Rep 2021; 35:108988. [PMID: 33852857 DOI: 10.1016/j.celrep.2021.108988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/13/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
How regulatory sequences control gene expression is fundamental for explaining phenotypes in health and disease. Regulatory elements must ultimately be understood within their genomic environment and development- or tissue-specific contexts. Because this is technically challenging, few regulatory elements have been characterized in vivo. Here, we use inducible Cas9 and multiplexed guide RNAs to create hundreds of mutations in enhancers/promoters and 3' UTRs of 16 genes in C. elegans. Our software crispr-DART analyzes indel mutations in targeted DNA sequencing. We quantify the impact of mutations on expression and fitness by targeted RNA sequencing and DNA sampling. When applying our approach to the lin-41 3' UTR, generating hundreds of mutants, we find that the two adjacent binding sites for the miRNA let-7 can regulate lin-41 expression independently of each other. Finally, we map regulatory genotypes to phenotypic traits for several genes. Our approach enables parallel analysis of regulatory sequences directly in animals.
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Affiliation(s)
- Jonathan J Froehlich
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Bora Uyar
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Margareta Herzog
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Kathrin Theil
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Petar Glažar
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany.
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157
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Frequent loss of heterozygosity in CRISPR-Cas9-edited early human embryos. Proc Natl Acad Sci U S A 2021; 118:2004832117. [PMID: 34050011 DOI: 10.1073/pnas.2004832117] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
CRISPR-Cas9 genome editing is a promising technique for clinical applications, such as the correction of disease-associated alleles in somatic cells. The use of this approach has also been discussed in the context of heritable editing of the human germ line. However, studies assessing gene correction in early human embryos report low efficiency of mutation repair, high rates of mosaicism, and the possibility of unintended editing outcomes that may have pathologic consequences. We developed computational pipelines to assess single-cell genomics and transcriptomics datasets from OCT4 (POU5F1) CRISPR-Cas9-targeted and control human preimplantation embryos. This allowed us to evaluate on-target mutations that would be missed by more conventional genotyping techniques. We observed loss of heterozygosity in edited cells that spanned regions beyond the POU5F1 on-target locus, as well as segmental loss and gain of chromosome 6, on which the POU5F1 gene is located. Unintended genome editing outcomes were present in ∼16% of the human embryo cells analyzed and spanned 4-20 kb. Our observations are consistent with recent findings indicating complexity at on-target sites following CRISPR-Cas9 genome editing. Our work underscores the importance of further basic research to assess the safety of genome editing techniques in human embryos, which will inform debates about the potential clinical use of this technology.
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158
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Reti D, O'Brien A, Wetzel P, Tay A, Bauer DC, Wilson LOW. GOANA: A Universal High-Throughput Web Service for Assessing and Comparing the Outcome and Efficiency of Genome Editing Experiments. CRISPR J 2021; 4:243-252. [PMID: 33876955 DOI: 10.1089/crispr.2020.0068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The increased development of functionally diverse and highly specialized genome editors has created the need for comparative analytics tools that are able to profile the mutational outcomes, particularly rare and complex outcomes, to assess the editor's applicability to different domains. To address this need, we have developed Generalizable On-target activity ANAlyzer (GOANA), a high-throughput web-based software for determining editing efficiency and cataloguing rare outcomes from next-generation sequencing data. GOANA calculates mutation frequency and outcomes relative to a supplied control sample. It is scalable to thousands of target sites across the entire genome and is 4,000% faster than CRISPResso2. Mutations are reported on a "per-read" level rather than individually, enabling the identification of co-occurring mutations. GOANA is editor agnostic and can be applied to data generated from any targeted editing experiment, including base editors. Requiring only that control and treated reads are aligned to the same reference, GOANA can handle data from any library preparation method, including pooled amplicon and whole-genome sequencing. As a proof of principle, we analyze two large data sets of CRISPR-Cas9 and CRISPR-Cas12a editing, demonstrating the power of GOANA and highlighting several key differences between the two enzymes. GOANA is available for use at https://gt-scan.csiro.au/goana/ and as a command line tool from https://github.com/BauerLab/GOANA.
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Affiliation(s)
- Daniel Reti
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organization, North Ryde, Australia; Department of Biomedical Sciences, Macquarie Park, Australia
| | - Aidan O'Brien
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organization, North Ryde, Australia; Department of Biomedical Sciences, Macquarie Park, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia; Department of Biomedical Sciences, Macquarie Park, Australia
| | - Pascal Wetzel
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organization, North Ryde, Australia; Department of Biomedical Sciences, Macquarie Park, Australia
| | - Aidan Tay
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organization, North Ryde, Australia; Department of Biomedical Sciences, Macquarie Park, Australia
| | - Denis C Bauer
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organization, North Ryde, Australia; Department of Biomedical Sciences, Macquarie Park, Australia.,Macquarie University, Department of Biomedical Sciences, Macquarie Park, Australia
| | - Laurence O W Wilson
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organization, North Ryde, Australia; Department of Biomedical Sciences, Macquarie Park, Australia
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159
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Ranjan G, Sehgal P, Sharma D, Scaria V, Sivasubbu S. Functional long non-coding and circular RNAs in zebrafish. Brief Funct Genomics 2021:elab014. [PMID: 33755040 DOI: 10.1093/bfgp/elab014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
The utility of model organisms to understand the function of a novel transcript/genes has allowed us to delineate their molecular mechanisms in maintaining cellular homeostasis. Organisms such as zebrafish have contributed a lot in the field of developmental and disease biology. Attributable to advancement and deep transcriptomics, many new transcript isoforms and non-coding RNAs such as long noncoding RNA (lncRNA) and circular RNAs (circRNAs) have been identified and cataloged in multiple databases and many more are yet to be identified. Various methods and tools have been utilized to identify lncRNAs/circRNAs in zebrafish using deep sequencing of transcriptomes as templates. Functional analysis of a few candidates such as tie1-AS, ECAL1 and CDR1as in zebrafish provides a prospective outline to approach other known or novel lncRNA/circRNA. New genetic alteration tools like TALENS and CRISPRs have helped in probing for the molecular function of lncRNA/circRNA in zebrafish. Further latest improvements in experimental and computational techniques offer the identification of lncRNA/circRNA counterparts in humans and zebrafish thereby allowing easy modeling and analysis of function at cellular level.
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160
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Lu Z, Yao X, Lyu P, Yadav M, Yoo K, Atala A, Lu B. Lentiviral Capsid-Mediated Streptococcus pyogenes Cas9 Ribonucleoprotein Delivery for Efficient and Safe Multiplex Genome Editing. CRISPR J 2021; 4:914-928. [PMID: 33733873 DOI: 10.1089/crispr.2020.0106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Transient expression of the CRISPR-Cas9 machinery is desirable to reduce the risks of off-targets and immune responses. Electroporation of Cas9 ribonucleoproteins (RNPs) is the most common delivery method to achieve transient Cas9 expression. Recently, retroviral capsids have been used for delivering Streptococcus pyogenes Cas9 RNPs, in which Cas9 was fused to the viral proteins. The fusion strategy may cause relative low capsid assembly efficiency. We recently developed virus-like particles (VLPs) consisting of lentiviral capsid and Staphylococcus aureus Cas9 RNPs using the specific interactions between aptamer and aptamer-binding protein (ABP), and obtained near-normal capsid assembly efficiency. Here we test whether highly active Streptococcus pyogenes Cas9 (SpCas9) RNP VLPs can be generated with high efficiency by aptamer/ABP interaction. We found that by optimizing the locations and types of aptamer used for single guide RNA modification, highly active SpCas9 RNP VLPs can be generated efficiently. VLP-delivered SpCas9 generated lower off-target insertions and deletions than SpCas9 RNPs delivered by electroporation. VLPs containing Cas9 from different species and targeting multiple genes can be efficiently prepared in single-particle preparation. Multiple-target VLPs were more efficient than the combination of single-target VLPs for simultaneous targeting of multiple genes. Thus, in addition to better safety features, the Cas9 VLPs are especially suited for multiplex genome editing. In summary, our VLPs offer safe, efficient, and flexible multiplex genome editing.
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Affiliation(s)
- Zuyan Lu
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA
| | - Xingang Yao
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Pin Lyu
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA
| | - Manish Yadav
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA
| | - Kyung Yoo
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA
| | - Baisong Lu
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA
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161
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Spector LP, Tiffany M, Ferraro NM, Abell NS, Montgomery SB, Kay MA. Evaluating the Genomic Parameters Governing rAAV-Mediated Homologous Recombination. Mol Ther 2021; 29:1028-1046. [PMID: 33248247 PMCID: PMC7934627 DOI: 10.1016/j.ymthe.2020.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/16/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors have the unique ability to promote targeted integration of transgenes via homologous recombination at specified genomic sites, reaching frequencies of 0.1%-1%. We studied genomic parameters that influence targeting efficiencies on a large scale. To do this, we generated more than 1,000 engineered, doxycycline-inducible target sites in the human HAP1 cell line and infected this polyclonal population with a library of AAV-DJ targeting vectors, with each carrying a unique barcode. The heterogeneity of barcode integration at each target site provided an assessment of targeting efficiency at that locus. We compared targeting efficiency with and without target site transcription for identical chromosomal positions. Targeting efficiency was enhanced by target site transcription, while chromatin accessibility was associated with an increased likelihood of targeting. ChromHMM chromatin states characterizing transcription and enhancers in wild-type K562 cells were also associated with increased AAV-HR efficiency with and without target site transcription, respectively. Furthermore, the amenability of a site to targeting was influenced by the endogenous transcriptional level of intersecting genes. These results define important parameters that may not only assist in designing optimal targeting vectors for genome editing, but also provide new insights into the mechanism of AAV-mediated homologous recombination.
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Affiliation(s)
- Laura P Spector
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Tiffany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole M Ferraro
- Biomedical Informatics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathan S Abell
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark A Kay
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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162
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de Alencastro G, Puzzo F, Pavel-Dinu M, Zhang F, Pillay S, Majzoub K, Tiffany M, Jang H, Sheikali A, Cromer MK, Meetei R, Carette JE, Porteus MH, Pekrun K, Kay MA. Improved Genome Editing through Inhibition of FANCM and Members of the BTR Dissolvase Complex. Mol Ther 2021; 29:1016-1027. [PMID: 33678249 DOI: 10.1016/j.ymthe.2020.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors have the unique property of being able to perform genomic targeted integration (TI) without inducing a double-strand break (DSB). In order to improve our understanding of the mechanism behind TI mediated by AAV and improve its efficiency, we performed an unbiased genetic screen in human cells using a promoterless AAV-homologous recombination (AAV-HR) vector system. We identified that the inhibition of the Fanconi anemia complementation group M (FANCM) protein enhanced AAV-HR-mediated TI efficiencies in different cultured human cells by ∼6- to 9-fold. The combined knockdown of the FANCM and two proteins also associated with the FANCM complex, RecQ-mediated genome instability 1 (RMI1) and Bloom DNA helicase (BLM) from the BLM-topoisomerase IIIα (TOP3A)-RMI (BTR) dissolvase complex (RMI1, having also been identified in our screen), led to the enhancement of AAV-HR-mediated TI up to ∼17 times. AAV-HR-mediated TI in the presence of a nuclease (CRISPR-Cas9) was also increased by ∼1.5- to 2-fold in FANCM and RMI1 knockout cells, respectively. Furthermore, knockdown of FANCM in human CD34+ hematopoietic stem and progenitor cells (HSPCs) increased AAV-HR-mediated TI by ∼3.5-fold. This study expands our knowledge on the mechanisms related to AAV-mediated TI, and it highlights new pathways that might be manipulated for future improvements in AAV-HR-mediated TI.
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Affiliation(s)
| | - Francesco Puzzo
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford, CA, USA
| | - Feijie Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Sirika Pillay
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Karim Majzoub
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Matthew Tiffany
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Hagoon Jang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Adam Sheikali
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford, CA, USA
| | - M Kyle Cromer
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford, CA, USA
| | - Ruhikanta Meetei
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Matthew H Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford, CA, USA
| | - Katja Pekrun
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Mark A Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA.
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163
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Turocy J, Adashi EY, Egli D. Heritable human genome editing: Research progress, ethical considerations, and hurdles to clinical practice. Cell 2021; 184:1561-1574. [PMID: 33740453 DOI: 10.1016/j.cell.2021.02.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/29/2021] [Accepted: 02/17/2021] [Indexed: 12/14/2022]
Abstract
Our genome at conception determines much of our health as an adult. Most human diseases have a heritable component and thus may be preventable through heritable genome editing. Preventing disease from the beginning of life before irreversible damage has occurred is an admirable goal, but the path to fruition remains unclear. Here, we review the significant scientific contributions to the field of human heritable genome editing, the unique ethical challenges that cannot be overlooked, and the hurdles that must be overcome prior to translating these technologies into clinical practice.
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Affiliation(s)
- Jenna Turocy
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Eli Y Adashi
- Professor of Medical Science, Brown University, Providence, RI, USA
| | - Dieter Egli
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA; Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
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164
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Weisheit I, Kroeger JA, Malik R, Wefers B, Lichtner P, Wurst W, Dichgans M, Paquet D. Simple and reliable detection of CRISPR-induced on-target effects by qgPCR and SNP genotyping. Nat Protoc 2021; 16:1714-1739. [PMID: 33597771 DOI: 10.1038/s41596-020-00481-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/09/2020] [Indexed: 01/31/2023]
Abstract
The recent CRISPR revolution has provided researchers with powerful tools to perform genome editing in a variety of organisms. However, recent reports indicate widespread occurrence of unintended CRISPR-induced on-target effects (OnTEs) at the edited site in mice and human induced pluripotent stem cells (iPSCs) that escape standard quality controls. By altering gene expression of targeted or neighbouring genes, OnTEs can severely affect phenotypes of CRISPR-edited cells and organisms and thus lead to data misinterpretation, which can undermine the reliability of CRISPR-based studies. Here we describe a broadly applicable framework for detecting OnTEs in genome-edited cells and organisms after non-homologous end joining-mediated and homology-directed repair-mediated editing. Our protocol enables identification of OnTEs such as large deletions, large insertions, rearrangements or loss of heterozygosity (LOH). This is achieved by subjecting genomic DNA first to quantitative genotyping PCR (qgPCR), which determines the number of intact alleles at the target site using the same PCR amplicon that has been optimized for genotyping. This combination of genotyping and quantitation makes it possible to exclude clones with monoallelic OnTEs and hemizygous editing, which are often mischaracterized as correctly edited in standard Sanger sequencing. Second, occurrence of LOH around the edited locus is detected by genotyping neighbouring single-nucleotide polymorphisms (SNPs), using either a Sanger sequencing-based method or SNP microarrays. All steps are optimized to maximize simplicity and minimize cost to promote wide dissemination and applicability across the field. The entire protocol from genomic DNA extraction to OnTE exclusion can be performed in 6-9 d.
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Affiliation(s)
- Isabel Weisheit
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU Munich, Planegg-Martinsried, Germany
| | - Joseph A Kroeger
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU Munich, Planegg-Martinsried, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Benedikt Wefers
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Institute of Developmental Genetics (IDG), HelmholtzZentrum München, Neuherberg, Germany
| | - Peter Lichtner
- Core Facility NGS, HelmholtzZentrum München, Neuherberg, Germany
| | - Wolfgang Wurst
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Institute of Developmental Genetics (IDG), HelmholtzZentrum München, Neuherberg, Germany
- Technische Universität München-Weihenstephan, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.
- Graduate School of Systemic Neurosciences, LMU Munich, Planegg-Martinsried, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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165
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Blondal T, Gamba C, Møller Jagd L, Su L, Demirov D, Guo S, Johnston CM, Riising EM, Wu X, Mikkelsen MJ, Szabova L, Mouritzen P. Verification of CRISPR editing and finding transgenic inserts by Xdrop indirect sequence capture followed by short- and long-read sequencing. Methods 2021; 191:68-77. [PMID: 33582298 DOI: 10.1016/j.ymeth.2021.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/12/2020] [Accepted: 02/02/2021] [Indexed: 01/02/2023] Open
Abstract
Validation of CRISPR-Cas9 editing typically explores the immediate vicinity of the gene editing site and distal off-target sequences, which has led to the conclusion that CRISPR-Cas9 editing is very specific. However, an increasing number of studies suggest that on-target unintended editing events like deletions and insertions are relatively frequent but unfortunately often missed in the validation of CRISPR-Cas9 editing. The deletions may be several kilobases-long and only affect one allele. The gold standard in molecular validation of gene editing is direct sequencing of relatively short PCR amplicons. This approach allows the detection of small editing events but fails in detecting large rearrangements, in particular when only one allele is affected. Detection of large rearrangements requires that an extended region is analyzed and the characterization of events may benefit from long-read sequencing. Here we implemented Xdrop™, a new microfluidic technology that allows targeted enrichment of long regions (~100 kb) using just a single standard PCR primer set. Sequencing of the enriched CRISPR-Cas9 gene-edited region in four cell lines on long- and short-read sequencing platforms unravelled unknown and unintended genome editing events. The analysis revealed accidental kilobases-large insertions in three of the cell lines, which remained undetected using standard procedures. We also applied the targeted enrichment approach to identify the integration site of a transgene in a mouse line. The results demonstrate the potential of this technology in gene editing validation as well as in more classic transgenics.
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Affiliation(s)
| | | | | | - Ling Su
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dimiter Demirov
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shuang Guo
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Ludmila Szabova
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, MD, USA
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166
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Huang TP, Newby GA, Liu DR. Precision genome editing using cytosine and adenine base editors in mammalian cells. Nat Protoc 2021; 16:1089-1128. [PMID: 33462442 DOI: 10.1038/s41596-020-00450-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/20/2020] [Indexed: 01/29/2023]
Abstract
Genome editing has transformed the life sciences and has exciting prospects for use in treating genetic diseases. Our laboratory developed base editing to enable precise and efficient genome editing while minimizing undesired byproducts and toxicity associated with double-stranded DNA breaks. Adenine and cytosine base editors mediate targeted A•T-to-G•C or C•G-to-T•A base pair changes, respectively, which can theoretically address most human disease-associated single-nucleotide polymorphisms. Current base editors can achieve high editing efficiencies-for example, approaching 100% in cultured mammalian cells or 70% in adult mouse neurons in vivo. Since their initial description, a large set of base editor variants have been developed with different on-target and off-target editing characteristics. Here, we describe a protocol for using base editing in cultured mammalian cells. We provide guidelines for choosing target sites, appropriate base editor variants and delivery strategies to best suit a desired application. We further describe standard base-editing experiments in HEK293T cells, along with computational analysis of base-editing outcomes using CRISPResso2. Beginning with target DNA site selection, base-editing experiments in mammalian cells can typically be completed within 1-3 weeks and require only standard molecular biology techniques and readily available plasmid constructs.
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Affiliation(s)
- Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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167
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Cetin R, Quandt E, Kaulich M. Functional Genomics Approaches to Elucidate Vulnerabilities of Intrinsic and Acquired Chemotherapy Resistance. Cells 2021; 10:cells10020260. [PMID: 33525637 PMCID: PMC7912423 DOI: 10.3390/cells10020260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Drug resistance is a commonly unavoidable consequence of cancer treatment that results in therapy failure and disease relapse. Intrinsic (pre-existing) or acquired resistance mechanisms can be drug-specific or be applicable to multiple drugs, resulting in multidrug resistance. The presence of drug resistance is, however, tightly coupled to changes in cellular homeostasis, which can lead to resistance-coupled vulnerabilities. Unbiased gene perturbations through RNAi and CRISPR technologies are invaluable tools to establish genotype-to-phenotype relationships at the genome scale. Moreover, their application to cancer cell lines can uncover new vulnerabilities that are associated with resistance mechanisms. Here, we discuss targeted and unbiased RNAi and CRISPR efforts in the discovery of drug resistance mechanisms by focusing on first-in-line chemotherapy and their enforced vulnerabilities, and we present a view forward on which measures should be taken to accelerate their clinical translation.
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Affiliation(s)
- Ronay Cetin
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany;
| | - Eva Quandt
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Barcelona, Spain;
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
- Correspondence: ; Tel.: +49-(0)-69-6301-5450
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168
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DGK and DZHK position paper on genome editing: basic science applications and future perspective. Basic Res Cardiol 2021; 116:2. [PMID: 33449167 PMCID: PMC7810637 DOI: 10.1007/s00395-020-00839-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022]
Abstract
For a long time, gene editing had been a scientific concept, which was limited to a few applications. With recent developments, following the discovery of TALEN zinc-finger endonucleases and in particular the CRISPR/Cas system, gene editing has become a technique applicable in most laboratories. The current gain- and loss-of function models in basic science are revolutionary as they allow unbiased screens of unprecedented depth and complexity and rapid development of transgenic animals. Modifications of CRISPR/Cas have been developed to precisely interrogate epigenetic regulation or to visualize DNA complexes. Moreover, gene editing as a clinical treatment option is rapidly developing with first trials on the way. This article reviews the most recent progress in the field, covering expert opinions gathered during joint conferences on genome editing of the German Cardiac Society (DGK) and the German Center for Cardiovascular Research (DZHK). Particularly focusing on the translational aspect and the combination of cellular and animal applications, the authors aim to provide direction for the development of the field and the most frequent applications with their problems.
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169
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Preece R, Pavesi A, Gkazi SA, Stegmann KA, Georgiadis C, Tan ZM, Aw JYJ, Maini MK, Bertoletti A, Qasim W. CRISPR-Mediated Base Conversion Allows Discriminatory Depletion of Endogenous T Cell Receptors for Enhanced Synthetic Immunity. Mol Ther Methods Clin Dev 2020; 19:149-161. [PMID: 33102612 PMCID: PMC7549055 DOI: 10.1016/j.omtm.2020.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/04/2020] [Indexed: 12/26/2022]
Abstract
Emerging base editing technology exploits CRISPR RNA-guided DNA modification effects for highly specific C > T conversion, which has been used to efficiently disrupt gene expression. These tools can enhance synthetic T cell immunity by restricting specificity, addressing histocompatibility leukocyte antigen (HLA) barriers, and promoting persistence. We report lentiviral delivery of a hepatitis B-virus (HBV)-specific recombinant T cell receptor (rTCR) and a linked CRISPR single-guide RNA for simultaneous disruption of endogenous TCRs (eTCRs) when combined with transient cytosine deamination. Discriminatory depletion of eTCR and coupled expression of rTCR resulted in enrichment of HBV-specific populations from 55% (SEM, ±2.4%) to 95% (SEM, ±0.5%). Intensity of rTCR expression increased 1.8- to 2.9-fold compared to that in cells retaining their competing eTCR, and increased cytokine production and killing of HBV antigen-expressing hepatoma cells in a 3D microfluidic model were exhibited. Molecular signatures confirmed that seamless conversion of C > T (G > A) had created a premature stop codon in TCR beta constant 1/2 loci, with no notable activity at predicted off-target sites. Thus, targeted disruption of eTCR by cytosine deamination and discriminatory enrichment of antigen-specific T cells offers the prospect of enhanced, more specific T cell therapies against HBV-associated hepatocellular carcinoma (HCC) as well as other viral and tumor antigens.
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Affiliation(s)
- Roland Preece
- Molecular and Cellular Immunology Unit, UCL Great Ormond Street Institute of Child Health, NIHR Great Ormond Street Hospital Biomedical Research Centre, 30 Guilford Street, London WC1N 1EH, UK
| | - Andrea Pavesi
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR) 61 Biopolis Drive, Singapore 138673, Singapore
| | - Soragia Athina Gkazi
- Molecular and Cellular Immunology Unit, UCL Great Ormond Street Institute of Child Health, NIHR Great Ormond Street Hospital Biomedical Research Centre, 30 Guilford Street, London WC1N 1EH, UK
| | - Kerstin A. Stegmann
- UCL Division of Infection and Immunity, The Rayne Building, 5 University Street, London WC1E 6EJ, UK
| | - Christos Georgiadis
- Molecular and Cellular Immunology Unit, UCL Great Ormond Street Institute of Child Health, NIHR Great Ormond Street Hospital Biomedical Research Centre, 30 Guilford Street, London WC1N 1EH, UK
| | - Zhi Ming Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR) 61 Biopolis Drive, Singapore 138673, Singapore
| | - Jia Ying Joey Aw
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR) 61 Biopolis Drive, Singapore 138673, Singapore
| | - Mala K. Maini
- UCL Division of Infection and Immunity, The Rayne Building, 5 University Street, London WC1E 6EJ, UK
| | - Antonio Bertoletti
- Program Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Singapore Immunology Network (SigN), Agency of Science Technology and Research (A∗STAR), Singapore, Singapore
| | - Waseem Qasim
- Molecular and Cellular Immunology Unit, UCL Great Ormond Street Institute of Child Health, NIHR Great Ormond Street Hospital Biomedical Research Centre, 30 Guilford Street, London WC1N 1EH, UK
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170
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Lau CH, Tin C, Suh Y. CRISPR-based strategies for targeted transgene knock-in and gene correction. Fac Rev 2020; 9:20. [PMID: 33659952 PMCID: PMC7886068 DOI: 10.12703/r/9-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The last few years have seen tremendous advances in CRISPR-mediated genome editing. Great efforts have been made to improve the efficiency, specificity, editing window, and targeting scope of CRISPR/Cas9-mediated transgene knock-in and gene correction. In this article, we comprehensively review recent progress in CRISPR-based strategies for targeted transgene knock-in and gene correction in both homology-dependent and homology-independent approaches. We cover homology-directed repair (HDR), synthesis-dependent strand annealing (SDSA), microhomology-mediated end joining (MMEJ), and homology-mediated end joining (HMEJ) pathways for a homology-dependent strategy and alternative DNA repair pathways such as non-homologous end joining (NHEJ), base excision repair (BER), and mismatch repair (MMR) for a homology-independent strategy. We also discuss base editing and prime editing that enable direct conversion of nucleotides in genomic DNA without damaging the DNA or requiring donor DNA. Notably, we illustrate the key mechanisms and design principles for each strategy, providing design guidelines for multiplex, flexible, scarless gene insertion and replacement at high efficiency and specificity. In addition, we highlight next-generation base editors that provide higher editing efficiency, fewer undesired by-products, and broader targeting scope.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
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171
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Bennett EP, Petersen BL, Johansen IE, Niu Y, Yang Z, Chamberlain CA, Met Ö, Wandall HH, Frödin M. INDEL detection, the 'Achilles heel' of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels. Nucleic Acids Res 2020; 48:11958-11981. [PMID: 33170255 PMCID: PMC7708060 DOI: 10.1093/nar/gkaa975] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 10/05/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Advances in genome editing technologies have enabled manipulation of genomes at the single base level. These technologies are based on programmable nucleases (PNs) that include meganucleases, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated 9 (Cas9) nucleases and have given researchers the ability to delete, insert or replace genomic DNA in cells, tissues and whole organisms. The great flexibility in re-designing the genomic target specificity of PNs has vastly expanded the scope of gene editing applications in life science, and shows great promise for development of the next generation gene therapies. PN technologies share the principle of inducing a DNA double-strand break (DSB) at a user-specified site in the genome, followed by cellular repair of the induced DSB. PN-elicited DSBs are mainly repaired by the non-homologous end joining (NHEJ) and the microhomology-mediated end joining (MMEJ) pathways, which can elicit a variety of small insertion or deletion (indel) mutations. If indels are elicited in a protein coding sequence and shift the reading frame, targeted gene knock out (KO) can readily be achieved using either of the available PNs. Despite the ease by which gene inactivation in principle can be achieved, in practice, successful KO is not only determined by the efficiency of NHEJ and MMEJ repair; it also depends on the design and properties of the PN utilized, delivery format chosen, the preferred indel repair outcomes at the targeted site, the chromatin state of the target site and the relative activities of the repair pathways in the edited cells. These variables preclude accurate prediction of the nature and frequency of PN induced indels. A key step of any gene KO experiment therefore becomes the detection, characterization and quantification of the indel(s) induced at the targeted genomic site in cells, tissues or whole organisms. In this survey, we briefly review naturally occurring indels and their detection. Next, we review the methods that have been developed for detection of PN-induced indels. We briefly outline the experimental steps and describe the pros and cons of the various methods to help users decide a suitable method for their editing application. We highlight recent advances that enable accurate and sensitive quantification of indel events in cells regardless of their genome complexity, turning a complex pool of different indel events into informative indel profiles. Finally, we review what has been learned about PN-elicited indel formation through the use of the new methods and how this insight is helping to further advance the genome editing field.
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Affiliation(s)
- Eric Paul Bennett
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Yiyuan Niu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, China
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | - Özcan Met
- Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Morten Frödin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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172
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Zhang M, Eshraghian EA, Jammal OA, Zhang Z, Zhu X. CRISPR technology: The engine that drives cancer therapy. Biomed Pharmacother 2020; 133:111007. [PMID: 33227699 DOI: 10.1016/j.biopha.2020.111007] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/04/2020] [Accepted: 11/08/2020] [Indexed: 02/07/2023] Open
Abstract
CRISPR gene editing technology belongs to the third generation of gene editing technology. Since its discovery, it has attracted the attention of a large number of researchers. Investigators have published a series of academic articles and obtained breakthrough research results through in-depth research. In recent years, this technology has developed rapidly and been widely applied in many fields, especially in medicine. This review focuses on concepts of CRISPR gene editing technology, its application in cancer treatments, its existing limitations, and the new progress in recent years for detailed analysis and sharing.
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Affiliation(s)
- Mingtao Zhang
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Emily A Eshraghian
- Department of Family Medicine and Public Health, School of Medicine, University of California San Diego, CA 92093, USA
| | - Omar Al Jammal
- Department of Family Medicine and Public Health, School of Medicine, University of California San Diego, CA 92093, USA
| | - Zhibi Zhang
- Biomedical Engineering Research Center, Kunming Medical University, Kunming, China.
| | - Xiao Zhu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China; The Key Lab of Zhanjiang for R&D Marine Microbial Resources in the Beibu Gulf Rim, Guangdong Medical University, Zhanjiang, China.
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173
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Zuccaro MV, Xu J, Mitchell C, Marin D, Zimmerman R, Rana B, Weinstein E, King RT, Palmerola KL, Smith ME, Tsang SH, Goland R, Jasin M, Lobo R, Treff N, Egli D. Allele-Specific Chromosome Removal after Cas9 Cleavage in Human Embryos. Cell 2020; 183:1650-1664.e15. [PMID: 33125898 DOI: 10.1016/j.cell.2020.10.025] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/02/2020] [Accepted: 10/14/2020] [Indexed: 12/24/2022]
Abstract
Correction of disease-causing mutations in human embryos holds the potential to reduce the burden of inherited genetic disorders and improve fertility treatments for couples with disease-causing mutations in lieu of embryo selection. Here, we evaluate repair outcomes of a Cas9-induced double-strand break (DSB) introduced on the paternal chromosome at the EYS locus, which carries a frameshift mutation causing blindness. We show that the most common repair outcome is microhomology-mediated end joining, which occurs during the first cell cycle in the zygote, leading to embryos with non-mosaic restoration of the reading frame. Notably, about half of the breaks remain unrepaired, resulting in an undetectable paternal allele and, after mitosis, loss of one or both chromosomal arms. Correspondingly, Cas9 off-target cleavage results in chromosomal losses and hemizygous indels because of cleavage of both alleles. These results demonstrate the ability to manipulate chromosome content and reveal significant challenges for mutation correction in human embryos.
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Affiliation(s)
- Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Jia Xu
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA
| | - Carl Mitchell
- Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Diego Marin
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA
| | | | - Bhavini Rana
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA; Department of Molecular Biosciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854, USA
| | - Everett Weinstein
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Rebeca T King
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Katherine L Palmerola
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Morgan E Smith
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Stephen H Tsang
- Columbia University Stem Cell Initiative, New York, NY 10032, USA; Departments of Ophthalmology, Pathology & Cell Biology, Columbia University. New York, NY, 10032, USA
| | - Robin Goland
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Rogerio Lobo
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Nathan Treff
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA; Department of Molecular Biosciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA.
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174
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Ophinni Y, Miki S, Hayashi Y, Kameoka M. Multiplexed tat-Targeting CRISPR-Cas9 Protects T Cells from Acute HIV-1 Infection with Inhibition of Viral Escape. Viruses 2020; 12:E1223. [PMID: 33126728 PMCID: PMC7693572 DOI: 10.3390/v12111223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 11/23/2022] Open
Abstract
HIV-1 cure strategy by means of proviral knock-out using CRISPR-Cas9 has been hampered by the emergence of viral resistance against the targeting guide RNA (gRNA). Here, we proposed multiple, concentrated gRNA attacks against HIV-1 regulatory genes to block viral escape. The T cell line were transduced with single and multiple gRNAs targeting HIV-1 tat and rev using lentiviral-based CRISPR-Cas9, followed by replicative HIV-1NL4-3 challenge in vitro. Viral p24 rebound was observed for almost all gRNAs, but multiplexing three tat-targeting gRNAs maintained p24 suppression and cell viability, indicating the inhibition of viral escape. Multiplexed tat gRNAs inhibited acute viral replication in the 2nd round of infection, abolished cell-associated transmission to unprotected T cells, and maintained protection through 45 days, post-infection (dpi) after a higher dose of HIV-1 infection. Finally, we describe here for the first time the assembly of all-in-one lentiviral vectors containing three and six gRNAs targeting tat and rev. A single-vector tat-targeting construct shows non-inferiority to the tat-targeting multi-vector in low-dose HIV-1 infection. We conclude that Cas9-induced, DNA repair-mediated mutations in tat are sufficiently deleterious and deplete HIV-1 fitness, and multiplexed disruption of tat further limits the possibility of an escape mutant arising, thus elevating the potential of CRISPR-Cas9 to achieve a long-term HIV-1 cure.
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Affiliation(s)
- Youdiil Ophinni
- Division of Molecular Medicine and Medical Genetics, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Hyogo, Japan;
| | - Sayaka Miki
- Division of Global Infectious Diseases, Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe 654-0142, Hyogo, Japan; (S.M.); (M.K.)
| | - Yoshitake Hayashi
- Division of Molecular Medicine and Medical Genetics, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Hyogo, Japan;
| | - Masanori Kameoka
- Division of Global Infectious Diseases, Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe 654-0142, Hyogo, Japan; (S.M.); (M.K.)
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175
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Wang D, Zhang F, Gao G. CRISPR-Based Therapeutic Genome Editing: Strategies and In Vivo Delivery by AAV Vectors. Cell 2020; 181:136-150. [PMID: 32243786 DOI: 10.1016/j.cell.2020.03.023] [Citation(s) in RCA: 280] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/26/2022]
Abstract
The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-based biotechnologies has revolutionized the life sciences and introduced new therapeutic modalities with the potential to treat a wide range of diseases. Here, we describe CRISPR-based strategies to improve human health, with an emphasis on the delivery of CRISPR therapeutics directly into the human body using adeno-associated virus (AAV) vectors. We also discuss challenges facing broad deployment of CRISPR-based therapeutics and highlight areas where continued discovery and technological development can further advance these revolutionary new treatments.
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Affiliation(s)
- Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Brain and Cognitive Sciences, Department of Biological Engineering, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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176
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Zhang B. CRISPR/Cas gene therapy. J Cell Physiol 2020; 236:2459-2481. [PMID: 32959897 DOI: 10.1002/jcp.30064] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/25/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated enzyme (Cas) is a naturally occurring genome editing tool adopted from the prokaryotic adaptive immune defense system. Currently, CRISPR/Cas9-based genome editing has been becoming one of the most promising tools for treating human genetic diseases, including cardiovascular diseases, neuro-disorders, and cancers. As the quick modification of the CRISPR/Cas9 system, including delivery system, CRISPR/Cas9-based gene therapy has been extensively studied in preclinic and clinic treatments. CRISPR/Cas genome editing is also a robust tool to create animal genetic models for studying and treating human genetic disorders, particularly diseases associated with point mutations. However, significant challenges also remain before CRISPR/Cas technology can be routinely employed in the clinic for treating different genetic diseases, which include toxicity and immune response of treated cells to CRISPR/Cas component, highly throughput delivery method, and potential off-target impact. The off-target effect is one of the major concerns for CRISPR/Cas9 gene therapy, more research should be focused on limiting this impact by designing high specific gRNAs and using high specificity of Cas enzymes. Modifying the CRISPR/Cas9 delivery method not only targets a specific tissue/cell but also potentially limits the off-target impact.
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Affiliation(s)
- Baohong Zhang
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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177
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Watry HL, Feliciano CM, Gjoni K, Takahashi G, Miyaoka Y, Conklin BR, Judge LM. Rapid, precise quantification of large DNA excisions and inversions by ddPCR. Sci Rep 2020; 10:14896. [PMID: 32913194 PMCID: PMC7483445 DOI: 10.1038/s41598-020-71742-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
The excision of genomic sequences using paired CRISPR-Cas nucleases is a powerful tool to study gene function, create disease models and holds promise for therapeutic gene editing. However, our understanding of the factors that favor efficient excision is limited by the lack of a rapid, accurate measurement of DNA excision outcomes that is free of amplification bias. Here, we introduce ddXR (droplet digital PCR eXcision Reporter), a method that enables the accurate and sensitive detection of excisions and inversions independent of length. The method can be completed in a few hours without the need for next-generation sequencing. The ddXR method uncovered unexpectedly high rates of large (> 20 kb) excisions and inversions, while also revealing a surprisingly low dependence on linear distance, up to 170 kb. We further modified the method to measure precise repair of excision junctions and allele-specific excision, with important implications for disease modeling and therapeutic gene editing.
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Affiliation(s)
- Hannah L Watry
- Gladstone Institute of Data Sciences and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Carissa M Feliciano
- Gladstone Institute of Data Sciences and Biotechnology, San Francisco, CA, USA
- Department of Pediatrics, UCSF, San Francisco, CA, USA
| | - Ketrin Gjoni
- Gladstone Institute of Data Sciences and Biotechnology, San Francisco, CA, USA
| | - Gou Takahashi
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yuichiro Miyaoka
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Bruce R Conklin
- Gladstone Institute of Data Sciences and Biotechnology, San Francisco, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- Department of Ophthalmology, UCSF, San Francisco, CA, USA.
- Department of Medicine, UCSF, San Francisco, CA, USA.
| | - Luke M Judge
- Gladstone Institute of Data Sciences and Biotechnology, San Francisco, CA, USA.
- Department of Pediatrics, UCSF, San Francisco, CA, USA.
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178
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Prat F, Toutain J, Boutin J, Amintas S, Cullot G, Lalanne M, Lamrissi-Garcia I, Moranvillier I, Richard E, Blouin JM, Dabernat S, Moreau-Gaudry F, Bedel A. Mutation-Specific Guide RNA for Compound Heterozygous Porphyria On-target Scarless Correction by CRISPR/Cas9 in Stem Cells. Stem Cell Reports 2020; 15:677-693. [PMID: 32795423 PMCID: PMC7486222 DOI: 10.1016/j.stemcr.2020.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 01/31/2023] Open
Abstract
CRISPR/Cas9 is a promising technology for gene correction. However, the edition is often biallelic, and uncontrolled small insertions and deletions (indels) concomitant to precise correction are created. Mutation-specific guide RNAs were recently tested to correct dominant inherited diseases, sparing the wild-type allele. We tested an original approach to correct compound heterozygous recessive mutations. We compared editing efficiency and genotoxicity by biallelic guide RNA versus mutant allele-specific guide RNA in iPSCs derived from a congenital erythropoietic porphyria patient carrying compound heterozygous mutations resulting in UROS gene invalidation. We obtained UROS function rescue and metabolic correction with both guides with the potential of use for porphyria clinical intervention. However, unlike the biallelic one, the mutant allele-specific guide was free of on-target collateral damage. We recommend this design to avoid genotoxicity and to obtain on-target scarless gene correction for recessive disease with frequent cases of compound heterozygous mutations.
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Affiliation(s)
- Florence Prat
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France
| | - Jérôme Toutain
- Medical Genetic Laboratory, CHU Bordeaux, Bordeaux 33000, France
| | - Julian Boutin
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France
| | - Samuel Amintas
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Laboratory of Tumor Biology, CHU Bordeaux, Pessac 33604, France
| | - Grégoire Cullot
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France
| | - Magalie Lalanne
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France
| | - Isabelle Lamrissi-Garcia
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France
| | | | - Emmanuel Richard
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Biochemistry Laboratory, CHU Bordeaux, Bordeaux 33000, France; Laboratory of Excellence, GR-Ex, Imagine Institute, Paris 75015, France
| | - Jean-Marc Blouin
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Biochemistry Laboratory, CHU Bordeaux, Bordeaux 33000, France; Laboratory of Excellence, GR-Ex, Imagine Institute, Paris 75015, France
| | - Sandrine Dabernat
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Biochemistry Laboratory, CHU Bordeaux, Bordeaux 33000, France; Laboratory of Excellence, GR-Ex, Imagine Institute, Paris 75015, France
| | - François Moreau-Gaudry
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Biochemistry Laboratory, CHU Bordeaux, Bordeaux 33000, France; Laboratory of Excellence, GR-Ex, Imagine Institute, Paris 75015, France
| | - Aurélie Bedel
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Biochemistry Laboratory, CHU Bordeaux, Bordeaux 33000, France; Laboratory of Excellence, GR-Ex, Imagine Institute, Paris 75015, France.
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179
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180
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Newman A, Starrs L, Burgio G. Cas9 Cuts and Consequences; Detecting, Predicting, and Mitigating CRISPR/Cas9 On- and Off-Target Damage: Techniques for Detecting, Predicting, and Mitigating the On- and off-target Effects of Cas9 Editing. Bioessays 2020; 42:e2000047. [PMID: 32643177 DOI: 10.1002/bies.202000047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/12/2020] [Indexed: 12/12/2022]
Abstract
Large deletions and genomic re-arrangements are increasingly recognized as common products of double-strand break repair at Clustered Regularly Interspaced, Short Palindromic Repeats - CRISPR associated protein 9 (CRISPR/Cas9) on-target sites. Together with well-known off-target editing products from Cas9 target misrecognition, these are important limitations, that need to be addressed. Rigorous assessment of Cas9-editing is necessary to ensure validity of observed phenotypes in Cas9-edited cell-lines and model organisms. Here the mechanisms of Cas9 specificity, and strategies to assess and mitigate unwanted effects of Cas9 editing are reviewed; covering guide-RNA design, RNA modifications, Cas9 modifications, control of Cas9 activity; computational prediction for off-targets, and experimental methods for detecting Cas9 cleavage. Although recognition of the prevalence of on- and off-target effects of Cas9 editing has increased in recent years, broader uptake across the gene editing community will be important in determining the specificity of Cas9 across diverse applications and organisms.
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Affiliation(s)
- Anthony Newman
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
| | - Lora Starrs
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
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181
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Edgington MP, Harvey‐Samuel T, Alphey L. Population-level multiplexing: A promising strategy to manage the evolution of resistance against gene drives targeting a neutral locus. Evol Appl 2020; 13:1939-1948. [PMID: 32908596 PMCID: PMC7463328 DOI: 10.1111/eva.12945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 01/30/2023] Open
Abstract
CRISPR-based gene drives bias inheritance in their favour by inducing double-stranded breaks (DSBs) at wild-type homologous loci and using the drive transgene as a repair template-converting drive heterozygotes into homozygotes. Recent studies have shown that alternate end-joining repair mechanisms produce cut-resistant alleles that rapidly induce drive failure. Multiplexing-simultaneously targeting multiple sites at the wild-type locus-is commonly assumed to overcome this issue since resistance would need to develop at all target sites for the system to fail. This may work for some population suppression drives targeting essential (e.g. viability or fertility) genes if careful design can ensure cut-resistant alleles themselves have low fitness. However, here, models are used to demonstrate that this approach will be ineffective when targeting neutral loci. We then go on to compare the performance of four alternative population-level multiplexing approaches with standard individual-level multiplexing. Two of these approaches have mechanisms preventing them from becoming linked, thus avoiding multiple simultaneous DSBs and giving a large improvement. Releasing multiple unlinked drives gives a modest improvement, while releasing multiple drives that may become linked over time produces a decrease in performance under the conditions tested here. Based on performance and technical feasibility, we then take one approach forward for further investigation, demonstrating its robustness to different performance parameters and its potential for controlling very large target populations.
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182
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Micol-Ponce R, García-Alcázar M, Capel C, Yuste-Lisbona FJ, Pineda B, Atarés A, García-Sogo B, Capel J, Moreno V, Lozano R. The Tomato SlVIPP1 Gene Is Required for Plant Survival Through the Proper Development of Chloroplast Thylakoid Membrane. FRONTIERS IN PLANT SCIENCE 2020; 11:1305. [PMID: 32983195 PMCID: PMC7479267 DOI: 10.3389/fpls.2020.01305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
Since membranes play essential roles in all living beings, all cells have developed mechanisms for efficient and fast repair of membrane damage. In Escherichia coli, the Phage shock stress A (PspA) protein is involved in the maintenance of the integrity of its inner membrane in response to the damage produced by exposure to stress conditions. A role in thylakoid membrane maintenance and reorganization has been proposed for Vesicle Inducing Protein in Plastid 1 (VIPP1), the putative PspA ortholog in Arabidopsis thaliana. While some membranes of plant cells have been extensively studied, the biosynthesis and maintenance of chloroplast thylakoid membrane remains poorly known. Here, we report the cloning and functional characterization of the tomato (Solanum lycopersicum L.) ortholog of Escherichia coli PspA and Arabidopsis thaliana VIPP1, which we dubbed SlVIPP1. Our genetic and molecular characterization of slvipp1, an insertional mutant, allowed us to conclude that the tomato SlVIPP1 gene is needed for development, as Arabidopsis VIPP1, but not Escherichia coli PspA. Homozygous slvipp1 tomato plants are albino and exhibit early lethality and highly aberrant chloroplast development with almost complete absence of thylakoids. The phenotype of tomato RNAi lines and that of additional slvipp1 alleles generated by CRISPR/Cas9 gene editing technology confirmed that the morphological and histological aberrations shown by slvipp1 homozygotes are caused by VIPP1 lack of function. We also found that tomato SlVIPP1 overexpression does not cause any visible effect on plant morphology and viability. Our work with slvipp1 plants evidences that SlVIPP1 is an essential gene required for tomato survival, since its function is crucial for the proper formation and/or maintenance of thylakoid membranes.
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Affiliation(s)
- Rosa Micol-Ponce
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
| | - Manuel García-Alcázar
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
| | - Carmen Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
| | | | - Benito Pineda
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | - Alejandro Atarés
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | - Begoña García-Sogo
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | - Juan Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
| | - Vicente Moreno
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
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183
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Meng D, Ragi SD, Tsang SH. Therapy in Rhodopsin-Mediated Autosomal Dominant Retinitis Pigmentosa. Mol Ther 2020; 28:2139-2149. [PMID: 32882181 DOI: 10.1016/j.ymthe.2020.08.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/22/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022] Open
Abstract
Rhodopsin-mediated autosomal dominant retinitis pigmentosa (RHO-adRP) is a hereditary degenerative disorder in which mutations in the gene encoding RHO, the light-sensitive G protein-coupled receptor involved in phototransduction in rods, lead to progressive loss of rods and subsequently cones in the retina. Clinical phenotypes are diverse, ranging from mild night blindness to severe visual impairments. There is currently no cure for RHO-adRP. Although there have been significant advances in gene therapy for inherited retinal diseases, treating RHO-adRP presents a unique challenge since it is an autosomal dominant disease caused by more than 150 gain-of-function mutations in the RHO gene, rendering the established gene supplementation strategy inadequate. This review provides an update on RNA therapeutics and therapeutic editing genome surgery strategies and ongoing clinical trials for RHO-adRP, discussing mechanisms of action, preclinical data, current state of development, as well as risk and benefit considerations. Potential outcome measures useful for future clinical trials are also addressed.
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Affiliation(s)
- Da Meng
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Sara D Ragi
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Medical Center, New York, NY 10032, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Medical Center, New York, NY 10032, USA; Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology & Cell Biology, Institute of Human Nutrition, Columbia Stem Cell Initiative, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY 10032, USA.
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184
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Bi C, Wang L, Yuan B, Zhou X, Li Y, Wang S, Pang Y, Gao X, Huang Y, Li M. Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs. Genome Biol 2020; 21:213. [PMID: 32831134 PMCID: PMC7444080 DOI: 10.1186/s13059-020-02143-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
Quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems. We develop a universal method to label individual DNA molecules for single-base-resolution haplotype-resolved quantitative characterization of diverse types of rare variants, with frequency as low as 4 × 10-5, using both short- or long-read sequencing platforms. It provides the first quantitative evidence of persistent nonrandom large structural variants and an increase in single-nucleotide variants at the on-target locus following repair of double-strand breaks induced by CRISPR-Cas9 in human embryonic stem cells.
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Affiliation(s)
- Chongwei Bi
- Laboratory of Stem Cell and Regeneration, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lin Wang
- Laboratory of Stem Cell and Regeneration, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Present address: Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Baolei Yuan
- Laboratory of Stem Cell and Regeneration, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Xuan Zhou
- Laboratory of Stem Cell and Regeneration, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yu Li
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Sheng Wang
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Yuhong Pang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Mo Li
- Laboratory of Stem Cell and Regeneration, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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185
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186
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Large-Fragment Deletions Induced by Cas9 Cleavage while Not in the BEs System. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:523-526. [PMID: 32711379 PMCID: PMC7381496 DOI: 10.1016/j.omtn.2020.06.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/12/2020] [Accepted: 06/22/2020] [Indexed: 11/20/2022]
Abstract
CRISPR-Cas9 and base editors (BEs) systems are poised to become the gene-editing tool of choice in clinical contexts; however, large-fragment deletion was found in Cas9-mediated mutation cells and mice. In this study, by analyzing 16 gene-edited rabbit lines (including 112 rabbits) generated using SpCas9, BEs, xCas9, and xCas9-BEs with long-range PCR genotyping and long-read sequencing by the PacBio platform, we show the extension of thousands of base fragment deletions in single-guide RNA/Cas9 and xCas9 system mutation rabbits, but no deletions were found in BE-induced mutation rabbits. Thus, we first validated that no large-fragment deletion was induced by the BEs system, suggesting that BE systems can be beneficial tools for the further development of highly accurate and secure gene therapy for the clinical treatment of human genetic disorders.
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187
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Burgio G. Gene conversion following CRISPR/Cas9 DNA cleavage: an overlooked effect. Gene Ther 2020; 27:245-246. [PMID: 32341482 DOI: 10.1038/s41434-020-0154-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 02/04/2023]
Affiliation(s)
- Gaetan Burgio
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
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188
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Bayraktar EC, La K, Karpman K, Unlu G, Ozerdem C, Ritter DJ, Alwaseem H, Molina H, Hoffmann HH, Millner A, Atilla-Gokcumen GE, Gamazon ER, Rushing AR, Knapik EW, Basu S, Birsoy K. Metabolic coessentiality mapping identifies C12orf49 as a regulator of SREBP processing and cholesterol metabolism. Nat Metab 2020; 2:487-498. [PMID: 32694732 PMCID: PMC7384252 DOI: 10.1038/s42255-020-0206-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/15/2020] [Indexed: 12/14/2022]
Abstract
Coessentiality mapping has been useful to systematically cluster genes into biological pathways and identify gene functions1-3. Here, using the debiased sparse partial correlation (DSPC) method3, we construct a functional coessentiality map for cellular metabolic processes across human cancer cell lines. This analysis reveals 35 modules associated with known metabolic pathways and further assigns metabolic functions to unknown genes. In particular, we identify C12orf49 as an essential regulator of cholesterol and fatty acid metabolism in mammalian cells. Mechanistically, C12orf49 localizes to the Golgi, binds membrane-bound transcription factor peptidase, site 1 (MBTPS1, site 1 protease) and is necessary for the cleavage of its substrates, including sterol regulatory element binding protein (SREBP) transcription factors. This function depends on the evolutionarily conserved uncharacterized domain (DUF2054) and promotes cell proliferation under cholesterol depletion. Notably, c12orf49 depletion in zebrafish blocks dietary lipid clearance in vivo, mimicking the phenotype of mbtps1 mutants. Finally, in an electronic health record (EHR)-linked DNA biobank, C12orf49 is associated with hyperlipidaemia through phenome analysis. Altogether, our findings reveal a conserved role for C12orf49 in cholesterol and lipid homeostasis and provide a platform to identify unknown components of other metabolic pathways.
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Affiliation(s)
- Erol C Bayraktar
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Konnor La
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Kara Karpman
- Center for Applied Mathematics, Cornell University, Ithaca, NY, USA
| | - Gokhan Unlu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Ceren Ozerdem
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Dylan J Ritter
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Alec Millner
- Department of Chemistry, University at Buffalo, The State University of New York (SUNY), Buffalo, NY, USA
| | - G Ekin Atilla-Gokcumen
- Department of Chemistry, University at Buffalo, The State University of New York (SUNY), Buffalo, NY, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amy R Rushing
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ela W Knapik
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Sumanta Basu
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA.
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189
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Ikeda M, Taniguchi-Ikeda M, Kato T, Shinkai Y, Tanaka S, Hagiwara H, Sasaki N, Masaki T, Matsumura K, Sonoo M, Kurahashi H, Saito F. Unexpected Mutations by CRISPR-Cas9 CTG Repeat Excision in Myotonic Dystrophy and Use of CRISPR Interference as an Alternative Approach. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 18:131-144. [PMID: 32637445 PMCID: PMC7321784 DOI: 10.1016/j.omtm.2020.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022]
Abstract
Myotonic dystrophy type 1 is the most common type of adult-onset muscular dystrophy. This is an autosomal dominant disorder and caused by the expansion of the CTG repeat in the 3′ untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. Messenger RNAs containing these expanded repeats form aggregates as nuclear RNA foci. Then, RNA binding proteins, including muscleblind-like 1, are sequestered to the RNA foci, leading to systemic abnormal RNA splicing. In this study, we used CRISPR-Cas9 genome editing to excise this CTG repeat. Dual cleavage at the 5′ and 3′ regions of the repeat using a conventional Cas9 nuclease and a double nicking with Cas9 nickase successfully excised the CTG repeat. Subsequently, the formation of the RNA foci was markedly reduced in patient-derived fibroblasts. However, contrary to expectations, a considerable amount of off-target digestions and on-target genomic rearrangements were observed using high-throughput genome-wide translocation sequencing. Finally, the suppression of DMPK transcripts using CRISPR interference significantly decreased the intensity of RNA foci. Our results indicate that close attention should be paid to the unintended mutations when double-strand breaks are generated by CRISPR-Cas9 for therapeutic purposes. Alternative approaches independent of double-strand breaks, including CRISPR interference, may be considered.
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Affiliation(s)
- Miki Ikeda
- Department of Neurology, School of Medicine, Teikyo University, Tokyo 1738606, Japan
| | - Mariko Taniguchi-Ikeda
- Department of Clinical Genetics, Fujita Health University Hospital, Aichi 4701192, Japan.,Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 4701192, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 4701192, Japan
| | - Yasuko Shinkai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 4701192, Japan
| | - Sonoko Tanaka
- Department of Neurology, School of Medicine, Teikyo University, Tokyo 1738606, Japan
| | - Hiroki Hagiwara
- Department of Medical Science, Teikyo University of Science, Uenohara Campus, Yamanashi 4090193, Japan
| | - Naomichi Sasaki
- Department of Medical Science, Teikyo University of Science, Senju Campus, Tokyo 1200045, Japan
| | - Toshihiro Masaki
- Department of Medical Science, Teikyo University of Science, Senju Campus, Tokyo 1200045, Japan
| | - Kiichiro Matsumura
- Department of Neurology, School of Medicine, Teikyo University, Tokyo 1738606, Japan
| | - Masahiro Sonoo
- Department of Neurology, School of Medicine, Teikyo University, Tokyo 1738606, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 4701192, Japan
| | - Fumiaki Saito
- Department of Neurology, School of Medicine, Teikyo University, Tokyo 1738606, Japan
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190
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On-Target CRISPR/Cas9 Activity Can Cause Undesigned Large Deletion in Mouse Zygotes. Int J Mol Sci 2020; 21:ijms21103604. [PMID: 32443745 PMCID: PMC7279260 DOI: 10.3390/ijms21103604] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
Genome engineering has been tremendously affected by the appearance of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9)-based approach. Initially discovered as an adaptive immune system for prokaryotes, the method has rapidly evolved over the last decade, overtaking multiple technical challenges and scientific tasks and becoming one of the most effective, reliable, and easy-to-use technologies for precise genomic manipulations. Despite its undoubtable advantages, CRISPR/Cas9 technology cannot ensure absolute accuracy and predictability of genomic editing results. One of the major concerns, especially for clinical applications, is mutations resulting from error-prone repairs of CRISPR/Cas9-induced double-strand DNA breaks. In some cases, such error-prone repairs can cause unpredicted and unplanned large genomic modifications within the CRISPR/Cas9 on-target site. Here we describe the largest, to the best of our knowledge, undesigned on-target deletion with a size of ~293 kb that occurred after the cytoplasmic injection of CRISPR/Cas9 system components into mouse zygotes and speculate about its origin. We suppose that deletion occurred as a result of the truncation of one of the ends of a double-strand break during the repair.
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191
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Wang Z, Wang Y, Wang S, Gorzalski AJ, McSwiggin H, Yu T, Castaneda-Garcia K, Prince B, Wang H, Zheng H, Yan W. Efficient genome editing by CRISPR-Mb3Cas12a in mice. J Cell Sci 2020; 133:133/9/jcs240705. [PMID: 32393674 DOI: 10.1242/jcs.240705] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
As an alternative and complementary approach to Cas9-based genome editing, Cas12a has not been widely used in mammalian cells largely due to its strict requirement for the TTTV protospacer adjacent motif (PAM) sequence. Here, we report that Mb3Cas12a (Moraxella bovoculi AAX11_00205) can efficiently edit the mouse genome based on the TTV PAM sequence with minimal numbers of large on-target deletions or insertions. When TTTV PAM sequence-targeting CRISPR (cr)RNAs of 23 nt spacers are used, >70% of the founders obtained are edited. Moreover, the use of Mb3Cas12a tagged to monomeric streptavidin (mSA) in conjunction with biotinylated DNA donor template leads to high knock-in efficiency in two-cell mouse embryos, with 40% of founders obtained containing the desired knock-in sequences.
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Affiliation(s)
- Zhuqing Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Yue Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Shawn Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Andrew J Gorzalski
- Nevada State Public Health Laboratory, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Hayden McSwiggin
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Tian Yu
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Kimberly Castaneda-Garcia
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Brian Prince
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Hetan Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA .,Department of Obstetrics and Gynecology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.,Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
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192
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Detection of Deleterious On-Target Effects after HDR-Mediated CRISPR Editing. Cell Rep 2020; 31:107689. [DOI: 10.1016/j.celrep.2020.107689] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 01/27/2023] Open
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193
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Safier LZ, Zuccaro MV, Egli D. Efficient SNP editing in haploid human pluripotent stem cells. J Assist Reprod Genet 2020; 37:735-745. [PMID: 32162131 PMCID: PMC7183036 DOI: 10.1007/s10815-020-01723-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To correct a potentially damaging mutation in haploid human embryonic stem cells. METHODS Exome sequencing was performed on DNA extracted from parthenogenetically derived embryonic stem cell line (pES12). An SLC10A2 gene mutation, which affects bile acid transport, was chosen as mutation of interest in this proof of concept study to attempt correction in human pluripotent haploid cells. Confirmation of the mutation was verified, and guide RNA and a correction template was designed in preparation of performing CRISPR. Haploid cells underwent serial fluorescence activated cell sorting (FACS) with Hoechst 33342 to create an increasingly haploid (1n) enriched culture. Nucleofection was performed on p. 37 and then cells were sorted for 1n DNA content with +GFP to identify the haploid cells that expressed Cas9 tagged with GFP. RESULTS 104,686 haploid GFP + cells were collected. Cells were cultured, individual colonies picked, and 48 clones were sent for Sanger sequencing. CRIPSR efficiency was 77.1%, with 7/48 (14.6%) clones resulting in a corrected SLC10A2 mutation. Confirmation of persistence of haploid cells was achieved with repeated FACS sorting and centromere quantification. Given the large number of passages and exposure to CRISPR, we also performed analysis of karyotypes and of off-target effects. Cells evaluated were karyotypically normal and there was no evident off target effects. CONCLUSIONS CRISPR/Cas9 can be effectively utilized to edit mutations in haploid human embryonic stem cells. Establishment and maintenance of a haploid cell culture provides a novel way to utilize CRISPR/Cas9 in gene editing, particularly in the study of recessive alleles.
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Affiliation(s)
- Lauren Zakarin Safier
- Department of Obstetrics and Gynecology and Columbia University Fertility Center, Columbia University, College of Physicians & Surgeons, New York, NY 10032 USA
- Present Address: Island Fertility, Stony Brook Medicine, 500 Commack Road, Suite 202, Commack, NY 11725 USA
| | - Michael V Zuccaro
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032 USA
| | - Dietrich Egli
- Department of Obstetrics and Gynecology, Columbia University, New York, NY USA
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032 USA
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194
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Xu M. CCR5-Δ32 biology, gene editing, and warnings for the future of CRISPR-Cas9 as a human and humane gene editing tool. Cell Biosci 2020; 10:48. [PMID: 32257106 PMCID: PMC7106751 DOI: 10.1186/s13578-020-00410-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/14/2020] [Indexed: 02/06/2023] Open
Abstract
Background Biomedical technologies have not just improved human health but also assisted in the creation of human life. Since the first birth of a healthy baby by in vitro fertilization (IVF) 40 years ago, IVF has been the mainstay treatment for couples struggling with infertility. This technology, in addition to increasingly accessible genetic testing, has made it possible for countless couples to have children. Since CRISPR-Cas9 gene editing was described in 2015, its potential for targeting genetic diseases has been much anticipated. However, the potential of using CRISPR-Cas9 for human germline modification has led to many fears of "designer babies" and widespread concerns for the impact of this technology on human evolution and its implications in Social Darwinism. In addition to these ethical/moral concerns, there remain many unknowns about CRISPR-Cas9 technology and endless unanticipated consequence to gene editing. Methods In this paper, we analyze the current progresses of CRISPR-Cas9 technology and discuss the theoretical advantages of certain allelic variances in the C-C chemokine receptor 5 gene (CCR5) in the setting of recent ethical/moral concerns regarding gene editing using the CRISPR-Cas9 system. Results These uncertainties have been highlighted recently by the birth of Chinese twins whose C-C chemokine receptor 5 (CCR5) gene had been inactivated via CRISPR-Cas9 to be theoretically protective against HIV infection. CCR5 signaling is critical for the successful infection of human immunodeficiency virus (HIV) and people with homozygous inactivating CCR5-Δ32 mutations have been shown to be protected against HIV infection. Those with the CCR5-Δ32/Δ32 mutation also have greater neuroplasticity, allowing for improved recovery from neurological trauma, and decreased Chagas cardiomyopathy. However, the CCR5-Δ32/Δ32 mutation has also been associated with earlier clinical manifestations for West Nile infection, ambiguous effects on osteoclast function, and a four-fold increased mortality from influenza infection. These detrimental health impacts, in addition to the confounding factor that these CRISPR babies do not carry this exact CCR5-Δ32/Δ32 mutation, lead to many questions regarding the children's future health and the moral conundrum of their birth. The creation and birth of these babies was not completed with any scientific, ethical, or governmental oversight, which has spurned the acceleration of talks regarding global regulations for human genetic editing. Conclusions Although we can try to regulate for ethical, health-related only use of this technology, moral and governmental oversights need to be supplemented by technical regulations. For instance, whole genome sequencing needs to be used to eliminate off-target mutations that could affect the health and safety of infants born to this process. Like Pandora's Box, we cannot pretend to forget CRISPR-Cas9 technology, all we can do is ensure a safe, moral, and equitable used of this technology.
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Affiliation(s)
- MengMeng Xu
- Department of Pediatrics, Morgan Stanley Children's Hospital, Columbia University, 3959 Broadway, New York, NY 10032 USA
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195
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Lee H, Yoon DE, Kim K. Genome editing methods in animal models. Anim Cells Syst (Seoul) 2020; 24:8-16. [PMID: 32158611 PMCID: PMC7048190 DOI: 10.1080/19768354.2020.1726462] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/03/2020] [Indexed: 12/15/2022] Open
Abstract
Genetically engineered animal models that reproduce human diseases are very important for the pathological study of various conditions. The development of the clustered regularly interspaced short palindromic repeats (CRISPR) system has enabled a faster and cheaper production of animal models compared with traditional gene-targeting methods using embryonic stem cells. Genome editing tools based on the CRISPR-Cas9 system are a breakthrough technology that allows the precise introduction of mutations at the target DNA sequences. In particular, this accelerated the creation of animal models, and greatly contributed to the research that utilized them. In this review, we introduce various strategies based on the CRISPR-Cas9 system for building animal models of human diseases and describe various in vivo delivery methods of CRISPR-Cas9 that are applied to disease models for therapeutic purposes. In addition, we summarize the currently available animal models of human diseases that were generated using the CRISPR-Cas9 system and discuss future directions.
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Affiliation(s)
- Hyunji Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Da Eun Yoon
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.,Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyoungmi Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.,Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
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196
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Castelletto ML, Gang SS, Hallem EA. Recent advances in functional genomics for parasitic nematodes of mammals. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb206482. [PMID: 32034038 DOI: 10.1242/jeb.206482] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human-parasitic nematodes infect over a quarter of the world's population and are a major cause of morbidity in low-resource settings. Currently available treatments have not been sufficient to eliminate infections in endemic areas, and drug resistance is an increasing concern, making new treatment options a priority. The development of new treatments requires an improved understanding of the basic biology of these nematodes. Specifically, a better understanding of parasitic nematode development, reproduction and behavior may yield novel drug targets or new opportunities for intervention such as repellents or traps. Until recently, our ability to study parasitic nematode biology was limited because few tools were available for their genetic manipulation. This is now changing as a result of recent advances in the large-scale sequencing of nematode genomes and the development of new techniques for their genetic manipulation. Notably, skin-penetrating gastrointestinal nematodes in the genus Strongyloides are now amenable to transgenesis, RNAi and CRISPR/Cas9-mediated targeted mutagenesis, positioning the Strongyloides species as model parasitic nematode systems. A number of other mammalian-parasitic nematodes, including the giant roundworm Ascaris suum and the tissue-dwelling filarial nematode Brugia malayi, are also now amenable to transgenesis and/or RNAi in some contexts. Using these tools, recent studies of Strongyloides species have already provided insight into the molecular pathways that control the developmental decision to form infective larvae and that drive the host-seeking behaviors of infective larvae. Ultimately, a mechanistic understanding of these processes could lead to the development of new avenues for nematode control.
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Affiliation(s)
- Michelle L Castelletto
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Spencer S Gang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92161, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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197
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Javidi-Parsijani P, Lyu P, Makani V, Sarhan WM, Yoo KW, El-Korashi L, Atala A, Lu B. CRISPR/Cas9 increases mitotic gene conversion in human cells. Gene Ther 2020; 27:281-296. [PMID: 32020049 DOI: 10.1038/s41434-020-0126-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 01/09/2020] [Accepted: 01/27/2020] [Indexed: 12/25/2022]
Abstract
Gene conversion is a process of transferring genetic material from one homologous sequence to another. Most reported gene conversions are meiotic although mitotic gene conversion is also described. When using CRISPR/Cas9 to target the human hemoglobin subunit beta (HBB) gene, hemoglobin subunit delta (HBD) gene footprints were observed in HBB gene. However, it is unclear whether these were the results of gene conversion or PCR-mediated sequence shuffling between highly homologous sequences. Here we provide evidence that the HBD footprints in HBB were indeed results of gene conversion. We demonstrated that the CRISPR/Cas9 facilitated unidirectional sequence transfer from the homologous gene without double-strand breaks (DSB) to the one with DSBs, and showed that the rates of HBD footprint in HBB were positively correlated to the HBB insertion and deletion rates. We further showed that when targeting HBD gene, HBB footprints could also be observed in HBD gene. The mitotic gene conversion was observed not only in immortalized HEK293T cells, but also in human primary cells. Our work reveals mitotic gene conversion as an often overlooked effect of CRISPR/Cas9-mediated genome editing.
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Affiliation(s)
- Parisa Javidi-Parsijani
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Pin Lyu
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Vishruti Makani
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Walaa Mohamed Sarhan
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Kyung Whan Yoo
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Lobna El-Korashi
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Baisong Lu
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA.
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198
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Yuan H, Yu T, Wang L, Yang L, Zhang Y, Liu H, Li M, Tang X, Liu Z, Li Z, Lu C, Chen X, Pang D, Ouyang H. Efficient base editing by RNA-guided cytidine base editors (CBEs) in pigs. Cell Mol Life Sci 2020; 77:719-733. [PMID: 31302752 PMCID: PMC11105001 DOI: 10.1007/s00018-019-03205-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 06/11/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
Abstract
Cytidine base editors (CBEs) have been demonstrated to be useful for precisely inducing C:G-to-T:A base mutations in various organisms. In this study, we showed that the BE4-Gam system induced the targeted C-to-T base conversion in porcine blastocysts at an efficiency of 66.7-71.4% via the injection of a single sgRNA targeting a xeno-antigen-related gene and BE4-Gam mRNA. Furthermore, the efficiency of simultaneous three gene base conversion via the injection of three targeting sgRNAs and BE4-Gam mRNA into porcine parthenogenetic embryos was 18.1%. We also obtained beta-1,4-N-acetyl-galactosaminyl transferase 2, alpha-1,3-galactosyltransferase, and cytidine monophosphate-N-acetylneuraminic acid hydroxylase deficient pig by somatic cell nuclear transfer, which exhibited significantly decreased activity. In addition, a new CBE version (termed AncBE4max) was used to edit genes in blastocysts and porcine fibroblasts (PFFs) for the first time. While this new version demonstrated a three genes base-editing rate of 71.4% at the porcine GGTA1, B4galNT2, and CMAH loci, it increased the frequency of bystander edits, which ranged from 17.8 to 71.4%. In this study, we efficiently and precisely mutated bases in porcine blastocysts and PFFs using CBEs and successfully generated C-to-T and C-to-G mutations in pigs. These results suggest that CBEs provide a more simple and efficient method for improving economic traits, reducing the breeding cycle, and increasing disease tolerance in pigs, thus aiding in the development of human disease models.
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Affiliation(s)
- Hongming Yuan
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Tingting Yu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Lingyu Wang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Lin Yang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Yuanzhu Zhang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Huan Liu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Mengjing Li
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xiaochun Tang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Zhiquan Liu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Zhanjun Li
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Chao Lu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xue Chen
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Daxin Pang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China.
| | - Hongsheng Ouyang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China.
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199
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Xu W, Yang Y, Liu Y, Kang G, Wang F, Li L, Lv X, Zhao S, Yuan S, Song J, Wu Y, Feng F, He X, Zhang C, Song W, Zhao J, Yang J. Discriminated sgRNAs-Based SurroGate System Greatly Enhances the Screening Efficiency of Plant Base-Edited Cells. MOLECULAR PLANT 2020; 13:169-180. [PMID: 31634585 DOI: 10.1016/j.molp.2019.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/27/2019] [Accepted: 10/13/2019] [Indexed: 05/13/2023]
Abstract
The development of CRISPR/Cas9-mediated base editing has made genomic modification more efficient. However, selection of genetically modified cells from millions of treated cells, especially plant cells, is still challenging. In this study, an efficient surrogate reporter system based on a defective hygromycin resistance gene was established in rice to enrich base-edited cells. After step-by-step optimization, the Discriminated sgRNAs-based SurroGate system (DisSUGs) was established by artificially differentiating the editing abilities of a wild-type single guide RNA (sgRNA) targeting the surrogate reporter gene and an enhanced sgRNA targeting endogenous sites. The DisSUGs enhanced the efficiency of screening base-edited cells by 3- to 5-fold for a PmCDA1-based cytosine-to-tyrosine base editor (PCBE), and 2.5- to 6.5-fold for an adenine base editor (ABE) at endogenous targets. These targets showed editing efficiencies of <25% in the conventional systems. The DisSUGs greatly enhanced the frequency of homozygous substitutions and expanded the activity window slightly for both a PCBE and an ABE. Analyses of the total number of single-nucleotide variants from whole-genome sequencing revealed that, compared with the no-enrichment PCBE strategy, the DisSUGs did not alter the frequency of genome-wide sgRNA-independent off-target mutations, but slightly increased the frequency of target-dependent off-target mutations. Collectively, the DisSUGs developed in this study greatly enhances the efficiency of screening plant base-edited cells and will be a useful system in future applications.
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Affiliation(s)
- Wen Xu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Yongxing Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Ya Liu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Guiting Kang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Feipeng Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Lu Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Xinxin Lv
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Si Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Shuang Yuan
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Jinling Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Ying Wu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Feng Feng
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Xiaoqing He
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Chengwei Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China.
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China.
| | - Jinxiao Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100080, China.
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200
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Riesenberg S, Chintalapati M, Macak D, Kanis P, Maricic T, Pääbo S. Simultaneous precise editing of multiple genes in human cells. Nucleic Acids Res 2019; 47:e116. [PMID: 31392986 PMCID: PMC6821318 DOI: 10.1093/nar/gkz669] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/26/2019] [Accepted: 07/24/2019] [Indexed: 01/01/2023] Open
Abstract
When double-strand breaks are introduced in a genome by CRISPR they are repaired either by non-homologous end joining (NHEJ), which often results in insertions or deletions (indels), or by homology-directed repair (HDR), which allows precise nucleotide substitutions to be introduced if a donor oligonucleotide is provided. Because NHEJ is more efficient than HDR, the frequency with which precise genome editing can be achieved is so low that simultaneous editing of more than one gene has hitherto not been possible. Here, we introduced a mutation in the human PRKDC gene that eliminates the kinase activity of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This results in an increase in HDR irrespective of cell type and CRISPR enzyme used, sometimes allowing 87% of chromosomes in a population of cells to be precisely edited. It also allows for precise editing of up to four genes simultaneously (8 chromosomes) in the same cell. Transient inhibition of DNA-PKcs by the kinase inhibitor M3814 is similarly able to enhance precise genome editing.
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Affiliation(s)
- Stephan Riesenberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
| | - Manjusha Chintalapati
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
| | - Dominik Macak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
| | - Philipp Kanis
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
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